[OTDev] RDF in OpenTox
Christoph Helma helma at in-silico.chFri May 27 20:04:53 CEST 2011
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Dear All, Some time ago I made some benchmark tests, if I remember correctly the main results were - the most resource intensive task was to build and maintain the internal RDF tree of the library (this is at least true for redland and RDF.rb libraries). I suppose that a lot of indexing is going on to make tree traversal more efficient. Resource usage (CPU and memory scaled very unfavorable with the size _and_ the "bushiness" (ie. branching degree) of the RDF tree - the library implementation (redland in C, RDF.rb in ruby) has a small impact, but both versions were unusable for our datasets - RDF format (RDF/XML, Turtle, N3, JSON, ...) had only a minor impact - parsing times was reduced by several orders of magnitude with a custom parser that avoids complex data structures and indexing (not much fun to write and maintain). I am also not sure how well it scales, it has still the limitation that everything has to fit into memory. Best regards, Christoph On Fri, 27 May 2011 19:27:24 +0200, Egon Willighagen <egon.willighagen at gmail.com> wrote: > Dear Pantelis, > > On Fri, May 27, 2011 at 5:50 PM, chung <chvng at mail.ntua.gr> wrote: > > Some criticism on RDF from the experience we've gained in OpenTox : > > http://is.gd/qLJG3h . The article is not complete yet and will be > > enriched with more facts and diagrams. > > Please do, because right now you left out so much detail on what you > are in fact doing. I do appreciate your frustration, and the > difference is unacceptable. > > I have these questions: > > * RDF is not a format, while ARFF is for file format? you mix RDF and > RDF/XML as if they are the same thing; why? > * what RDF file format have you used? RDF/XML, as you later refer to? > * are you using reasoning, and if so why? moreover, you should not > compare a reasoning environment with a non-reasoning one (of course, > you'd see differences) > * what information is specified in the ARFF header? > * why aren't you using a vector annotation in RDF? > * how large is the file, and what are you doing to use 2GB of heap space? > * how large is your data set? > * what does your code look like? > > A fair comment would be take ARFF takes a short cut: it imposes > additional structure on the data, something you identify in your > report. RDF does not do that by itself. A vector environment does. > That does not mean that such is not possible with RDF. Have you > consider what options there are to introduce this vector restriction > into the computational framework, forced to use RDF? Do you believe it > is impossible to achieve that with RDF? Would you see it impossible to > define an ontology to capture vector notation, allowing you to specify > what each column in that vector represents? > > Now, given that you do see that option too, you would probably end up > with a ontology looking very much like the ARFF specification, but the > in RDF. > > In short, based on your report I really cannot judge of RDF is the > problem, because your results do not make such conclusion possible. > Instead, I rather think that you are running into a highly confounded > analysis where it is not possible to assign the slowness to any > factor. I think you are comparing two widely different data models, > one optimized for computation (ARFF) and one not (your current RDF/XML > file). Would that perhaps be the significant factor in the difference > in speed? > > I am looking forward to a more detailed report on the various involved > factors that determine the speed here, > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Institutet för miljömedicin > Karolinska Institutet (http://ki.se/imm) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > _______________________________________________ > Development mailing list > Development at opentox.org > http://www.opentox.org/mailman/listinfo/development
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